Eric J. Routman

EPISTASIS AS A SOURCE OF INCREASED ADDITIVE GENETIC VARIANCE AT POPULATION BOTTLENECKS

The role of epistasis in evolution and speciation has remained controversial. We use a new parameterization of physiological epistasis to examine the effects of epistasis on levels of additive genetic variance during a population bottleneck. We found that all forms of epistasis increase average additive genetic variance in finite populations derived from initial populations with intermediate allele frequencies. Average additive variance continues to increase over many generations, especially at larger population sizes (N = 32 to 64). Additive‐by‐additive epistasis is the most potent source of additive genetic variance in this situation, whereas dominance‐by‐dominance epistasis contributes smaller amounts of additive genetic variance. With additive‐by‐dominance epistasis, additive genetic variance decreases at a relatively high rate immediately after a population bottleneck, rebounding to higher levels after several generations. Empirical examples of epistasis for murine adult body weight based on measured genotypes are provided illustrating the varying effects of epistasis on additive genetic variance during population bottlenecks.

PLEIOTROPIC EFFECTS OF INDIVIDUAL GENE LOCI ON MANDIBULAR MORPHOLOGY

The genotypic basis of morphological variation is largely unknown. In this study we examine patterns of pleiotropic effects on mandibular morphology at individual gene loci to determine whether the pleiotropic effects of individual genes are restricted to functionally and developmentally related traits. Mandibular measurements were obtained from 480 mice from the F2 generation of an intercross between the LG/J and SM/J mouse strains. DNA was also extracted from these animals, and 76 microsatellite loci covering the autosomes were scored. Interval mapping was used to detect chromosomal locations with significant effects on various mandibular measurements. Sets of traits mapping to a common chromosomal region were considered as being affected by a single quantitative trait locus (QTL) for mandibular morphology. Thirty‐seven such chromosomal regions were identified spread throughout the autosomes. Gene effects were small to moderate with the allele derived from the LG/J strain typically leading to larger size. When dominance was present, the LG/J allele was typically dominant to the SM/J allele. Most loci affected restricted functional and developmental regions of the mandible. Of the 26 chromosomal regions affecting more than two traits, 50% affect the muscular processes of the ascending ramus, 27% affect the alveolar processes carrying the teeth, and 23% affect the whole mandible. Four additional locations affecting two traits had effects significantly associated with alveolar regions. Pleiotropic effects are typically restricted to morphologically integrated complexes.

Quantitative Trait Loci for Early‐ and Late‐Developing Skull Characters in Mice: A Test of the Genetic Independence Model of Morphological Integration

Quantitative genetical theory suggests that characters existing in developmentally or functionally integrated groups are expected to be genetically correlated because they share a common inheritance. The genetic independence model for the cause of this genetic integration predicts that pleiotropic effects of single genes are mostly restricted to the characters in these integrated groups. We tested this model by estimating the additive and dominance effects of quantitative trait loci (QTLs) affecting early‐ (cranial vault) and late‐developing (face) skeletal characters in F2 house mice originally derived from a cross of the Large and Small inbred strains. Interval mapping procedures were used that resulted in the identification of 26 QTLs on 17 of the 19 autosomes that significantly affected these characters. Additive, but not dominance, genotypic effects of many of these QTLs predominantly affected either the cranial vault or face characters, which supports the genetic independence model. Only two QTLs had positive pleiotropic effects on one group of characters but negative pleiotropic effects on the other (antagonistic pleiotropy).

GENE EFFECTS ON A QUANTITATIVE TRAIT: TWO-LOCUS EPISTATIC EFFECTS MEASURED AT MICROSATELLITE MARKERS AND AT ESTIMATED QTL

Most evolutionarily and agriculturally important traits are affected by many genes (quantitative trait loci, or QTL) of relatively small effect. Usually the genetics of these traits are examined by indirect statistical analysis of the covariance among relatives, rather than by direct analyses. We use new analytical and molecular techniques to examine nonadditive interactions of microsatellite markers and estimated QTL that influence adult body weight in mice. Offspring of a cross between a large inbred mouse strain (LG/J) and a small inbred strain (SM/J) were intercrossed to form a segregating F2 generation. Using 76 microsatellite markers and 19 estimated QTL, we estimate gene‐level epistasis and population‐level epistasis for body weight at 10 weeks for 534 F2 mice. Significant epistasis was found for large numbers of the two locus comparisons using both markers and previously detected QTL. There are many genes segregating for adult body weight in this cross and many of these genes appear to interact epistatically. The discovery of potentially extensive epistasis has important implications for evolutionary models.

A SEARCH FOR QUANTITATIVE TRAIT LOCI AFFECTING ASYMMETRY OF MANDIBULAR CHARACTERS IN MICE

An interval mapping procedure was used to search for and describe the effects of any quantitative trait loci (QTLs) for directional asymmetry (DA) and fluctuating asymmetry (FA) of 10 bilateral mandible characters in house mice. It was hypothesized that more QTLs would be found for DA than for FA, but that any discovered for FA should tend to exhibit dominance. All mandible characters were triply measured and 76 microsatellite markers were scored in an average of 471 mice from the F2 intercross of the Large (LG/J) and Small (SM/J) inbred strains. A total of 16 QTLs significantly affected DA in nine of the 10 mandible characters, and this was more than the 9.5 expected by chance alone. These QTLs were found on seven of the 19 chromosomes, often at or near locations of QTLs affecting the mean of the two sides for various dimensions on the mandible. It was concluded that there is genetical variability for DA in these characters, although its level was low (4.4% of the total variation in this particular F2 population). Eleven QTLs were detected for FA, suggesting that there is very little genetic variability for FA, at least as seen in the mandible characters in this particular F2 population. As hypothesized, however, these QTLs did tend to exhibit dominance.

AN EPISTATIC GENETIC BASIS FOR FLUCTUATING ASYMMETRY OF MANDIBLE SIZE IN MICE

Abstract The genetic basis of fluctuating asymmetry (FA), or nondirectional variation in the subtle differences between left and right sides of bilateral characters, continues to be of considerable theoretical interest. FA generally has been thought to arise from random noise during development and therefore to have a largely or entirely environmental origin. Whereas additive genetic variation for FA generally has been small and often insignificant, a number of investigators have hypothesized that interactions between loci, or epistasis, significantly influence FA. We tested this hypothesis by conducting a whole‐genome scan to detect any epistasis in FA of centroid size in the mandibles of more than 400 mice from an F2 intercross population formed from crossing the Large (LG/J) and Small (SM/J) inbred strains. Genotypic deviations were imputed at each site 2 cM apart on all 19 autosomes, and these and centroid size asymmetry values were used in canonical correlation analyses for each of the 171 possible pairs of 19 autosomes to identify the most probable sites for epistasis. Epistasis for centroid size asymmetry was abundant, occurring far more often than was expected by chance alone (there were 30 separate instances of epistasis at the 0.001 significance level, when only two were expected by chance alone). The contributions of epistasis from 30 pairwise combinations of loci tended to suppress the additive and dominance genetic variance, but greatly increased the epistatic genetic variance for FA in centroid size given the intermediate allele frequencies of an F2 intercross population.

Quantitative trait loci for body size components in mice

Do body size components, such as weights of internal organs and long bone lengths, with different functions and different developmental histories also have different genetic architectures and pleiotropic patterns? We examine murine quantitative trait loci (QTL) for necropsy weight, four long bone lengths, and four organ weights in the LG/J × SM/J intercross. Differences between trait categories were found in number of QTL, dominance, and pleiotropic patterns. Ninety-seven QTLs for individual traits were identified: 52 for long bone lengths, 30 for organ weights, and 15 for necropsy weight. Results for long bones are typically more highly significant than for organs. Organ weights were more frequently over- or underdominant than long bone lengths or necropsy weight. The single-trait QTLs map to 35 pleiotropic loci. Long bones are much more frequently affected in groups while organs tend to be affected singly or in pairs. Organs and long bones are found at the same locus in only 11 cases, 8 of which also include necropsy weight. Our results suggest mainly separate genetic modules for organ weights and long bone lengths, with a few loci that affect overall body size. Antagonistic pleiotropy, in which a locus has opposite effects on different characteristics, is uncommon.

Molecular systematics, hybridization, and phylogeography of the Bufo americanus complex in Eastern North America

We reconstruct phylogenetic relationships among a well-studied group of toads and find relationships that differ greatly from the current taxonomic understanding. We use mitochondrial sequences encoding ND1, tRNA(Leu(UUR)), and part of 16S to infer relationships among members of the Bufo americanus complex. Focusing on the four taxa that historically have been most problematic due to morphological similarity and hybridization in sympatry, we sample 150 individuals from multiple populations across each species geographic range. Our evidence conflicts with previous taxonomic hypotheses that were based on ability to hybridize, geographic distribution, and call variation. First, sequences from B. fowleri do not comprise the sister clade to sequences of B. woodhousii; therefore the previous classifications of B. fowleri as sister species to, or eastern subspecies of, B. woodhousii are both called into question. Second, sequences from B. americanus are more closely related to those of B. woodhousii than to those of B. terrestris, indicating that similar advertisement call characteristics evolved independently. Third, sequences of B. fowleri are paraphyletic, with sequences of B. terrestris embedded within. Lastly, sequences from B. fowleri cluster into three distinct mitochondrial clades, with some divergences corresponding to greater than 2mya. These clades are somewhat geographically structured, suggesting divergence in allopatry during the Pleistocene. These mitochondrial divergences are not accompanied by known phenotypic differences, however, suggesting either evolutionary stasis in morphology and behavior, cryptic phenotypic evolution, or that hybridization in secondary contact has homogenized phenotypic differences that may have arisen in allopatry.

Quantitative trait loci for fluctuating asymmetry of discrete skeletal characters in mice

Levels of fluctuating asymmetry (FA) are often taken as indicators of the degree to which genotypes differ in their ability to buffer genetic and environmental sources of variation. Interval mapping techniques were used to search for quantitative trait loci (QTLs) affecting directional asymmetry (DA) and fluctuating asymmetry (FA) in six bilateral discrete skeletal traits in house mice. These six characters as well as 76 microsatellite markers were scored in over 500 mice that resulted from crosses of F1 mice originally produced from matings of the Large (LG/J) and Small (SM/J) inbred strains. The number of QTLs affecting DA in each of the characters was no more than expected by chance alone so it was concluded that there was little evidence for individual genes affecting DA. There appeared to be a genetical basis for FA in these characters, however, because the number of QTLs significantly affecting FA (10 at the 5% level, three at the 1% level) was greater than expected by chance alone. The 10 QTLs significantly affecting FA in any given character were located on eight different chromosomes, mostly at locations for QTLs affecting other characters or DA in other characters. Their cumulative contribution to the total phenotypic variance was small, averaging only 3.9% per locus. Dominance genotypic values for these QTLs were more extreme than additive genotypic values, suggesting that heterozygotes at many loci are better buffered than homozygotes and that allelic interactions (dominance) may play an important role in the production of FA.

PARSIMONY, MOLECULAR EVOLUTION, AND BIOGEOGRAPHY: THE CASE OF THE NORTH AMERICAN GIANT SALAMANDER

To draw biogeographic conclusions about the Central Highlands region of the United States, we reconstructed the phylogeny of hellbender (Cryptobranchus alleganiensis) populations from restriction‐site variation in mtDNA. We were unable to root the phylogeny using an outgroup and therefore could not weight restriction‐site gains more heavily than site losses. As a result, maximum parsimony results in low phylogenetic resolution because of high levels of homoplasy in the data set. Use of a recently published algorithm based on an explicit model of molecular evolution yielded much greater resolution of the mtDNA relationships. This phylogeny indicates the two subspecies of hellbenders are paraphyletic with respect to one another. Hellbenders found in the southern Ozarks (C. a. bishopi) are either most closely related to populations of C. a. alleganiensis inhabiting the Tennessee River drainage or are so divergent that phylogenetic affinities are undetectable. Extremely low levels of divergence among mtDNA haplotypes found in populations from Pennsylvania, Indiana, Illinois, and the northern Missouri Ozarks suggest a recent, probably post‐Pleistocene, invasion of this region from a refugium in one of these areas. Biogeographic hypotheses of the causes and timing of hellbender distributions differ significantly from those postulated from analyses of fish species relationships. Possible reasons for the discrepancy are discussed.